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GradientBoostingRegressor always sets presort to auto #5857
In the call to super inside
referenced this issue
Nov 16, 2015
I'm suspecting that that PR introduced both of the issues. I think there is a check_X_y call which is causing the other issue which I missed since I was using smaller datasets. I've been swamped with a few presentations I have to do this week, but I'll be available to take a look at both soon.